Cooperative Transitions in DNA with No Separation of Strands

Иванов, В. И.; Minchenkova, L. E.; Minyat, E. E.; Schyolkina, A. K.

doi:10.1101/sqb.1983.047.01.029

Cited by 42 publications

(40 citation statements)

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“…The DNA backbone is stabilized mainly by the electrostatic interactions. Both subsystems coordinate mutually their conformations through the flexible sugar rings [1,2,8,9]. So, in modeling the transformations of the DNA double helix it is important to use the components for the description of internal conformational rearrangements and external transformation of macromolecule shape.…”

Section: Model Constructionmentioning

confidence: 99%

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Modeling B–A Transformations of the DNA Double Helix

Волков

2005

J Biol Phys

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Abstract. An approach to the description of DNA conformational transformations of B-A type is presented. Due to the consideration of joint motions of DNA structural elements the model for DNA transformation is constructed in the two-component form. One component is the degree of freedom of the elastic rod, and another component -the effective coordinate of the conformational transformation. In the model the internal and external components are interrelated, as it is characteristic for DNA B-A rearrangements. It is demonstrated that kinetic energy of the double helix transformations of heterogeneous DNA can be put in homogeneous form. In the frame of the developed approach the possible localized excitations in a static state are found to compare with the experiments on DNA B-A deformability. The comparison shows good qualitative agreement between theory and experiment. The conclusion is made that the found excitations in the DNA structure may be classified as static conformational solitons, and that such localized excitations may play the key role in the mechanisms of DNA intrinsic bending.

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Section: Model Constructionmentioning

confidence: 99%

“…According to the four-mass model approach [1][2][3][4][5][6][7][8][9][10][11][12] the basic conformational degrees of freedom for the DNA monomer link are the following. First, displacements of the nucleosides (nucleic bases together with sugar rings) as pendulums "suspended" to the backbone chain.…”

Section: Generalized Four-mass Modelmentioning

confidence: 99%

Modeling B–A Transformations of the DNA Double Helix

Волков

2005

J Biol Phys

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“…[1][2][3][4][5][6]can undergo a transition either in one step or in two steps: first an a) transition for segment [1][2][3][4] followed by a c) transition in segment [4][5][6]. For W<W3, the latter scheme will prevail.…”

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“…la, segment can change state by following either of two paths: by a c) transition in one step, or in two steps an a) transition for segment [5-61 followed by a b) transition for segment [4][5]. Again for W<W2 the latter two step process prevails.…”

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An algorithm for studying cooperative transitions in DNA

et al. 1986

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5UIjZjjBX: Cooperative transitions in DNA (B to Z, B to A, helix to coil, etc.) are known to depend strongly on nucleotide sequence. In general the change in free energy involved in the transition can be expressed as:where oa is a factor arising from the free energy associated with boundaries of different conformations along the molecule.This formula allows to infer a general algorithm with which DNA sequences can be partitioned into well defined domains in which under suitable conditions, base pairs change state cooperatively.The different partitions of the sequence that can be generated by varying the values of the physical parameters involved in the above formula, are shown to be embedded into a binary tree hierarchy.Application to a reliable prediction of Z-DNA antibody binding sites will be illustrated for the 0X174 genome. Possible biological implications are briefly discussed. (*)Nucleic acids may adopt a number of conformations: A, B, Z, coil, etc. and under appropriate physical conditions they can readily switch between two of these conformations: helix to coil, B to Z, B to A, etc. (1-5). These conformations, and transitions between two of them,are highly dependent on base composition since the value of the parameters monitoring the transition point (supercoiling, hydration, temperature etc.) varies over large ranges for different polymers (5-7).In natural DNA, alternating conformations were observed to appear in domains ie. continuous base pair (bp.) stretches with well defined location inside the sequence sharing a given conformation. Domain sequences allow for "mismatches": disrupted GC bp. in an AT rich coiled segment below the poly(GC) melting point (3), Z segments in supercoiled DNA with breaks in the alternance (*) Prograns mentioned in this paper are available on request.

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The origin of the A to B transition in DNA fibers and films

Lindsay¹,

Lee²,

Powell³

et al. 1988

Biopolymers

147

111

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SynopsisWe have studied the hydration of Na-DNA and Li-DNA fibers and films, measuring water contents, x-ray fiber diffraction patterns, low-frequency Raman spectra (below 100 cm-I), high-frequency Raman spectra (soO-lOOO cm-'), and swelling, as a function of relative humidity. Most samples gain weight equilibrium (though not conformational equilibrium) in one day. The volume occupied by a base pair as the DNA is hydrated (obtained from the x-ray and swelling data) shows anomalies for the case of Na-DNA in the region where the A-form occurs. Our Raman and x-ray data reproduce the well-known features of the established conformational transitions, but we find evidence in the Raman spectra and optical properties of a transition to what may be a disordered B-like conformation in Na-DNA below 40% relative humidity. We have studied the effects of crystallinity on the A to B transition. We find that the transition to the B-form is impeded in highly crystalline samples. In most samples, the transition occurs in three days (after putting the sample at 92% relative humidity) but in highly crystalline samples, the transition may take months. By comparing the high-frequency Raman spectra of highly ordered and disordered films, we show that the extent of crystallinity controls the amount of A-DNA formed when ethanol is used to dehydrate the films. We show that rapid dehydration (by laser heating) does not result in a B to A transition. A fiber that gives A-type x-ray reflections probably contains B-like material in noncrystalline regions. The low-frequency Raman spectrum is dominated by a band at about 25 cm-' in both Na-and Li-DNA. Another band is seen near 35 cm-l in Na-DNA at humidities where the sample is in the A-form. In contrast to earlier reports, we find that the Raman intensity does not depend on fiber orientation relative to the scattering vector. The "35-crn-'" band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the "25-cm-'" band appears in both W, VH and HV polarizations. These bands are all weaker in HH polarization. The "25-cm-'" band may be due to a shearing motion of the phosphates and their associated counterions, while the "35-cm-" band may be characteristic of A-DNA crystallites. We consider mass-loading, relaxational coupling to the hydration shell, and softening of interatomic potentials as possible explanations of the observed softening of the low-frequency Raman bands on hydration. Relaxation data suggest that the added water binds tightly (on these time scales) and a mass-loading model accounts for the observed softening rather well.We conclude that the A to B transition is not driven by softening of the "25-cm-'" band. Rather, it is most probably a consequence of crystal-packing forces, with the more regular A-form favored in crystals when these forces are strong. INTRODUCTIONThe earliest fiber diffraction studies established that DNA can take up secondary structures that differ dramatically. Sodium-salted fibers give ...

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Cooperative Transitions in DNA with No Separation of Strands

Cited by 42 publications

References 1 publication

Modeling B–A Transformations of the DNA Double Helix

Modeling B–A Transformations of the DNA Double Helix

An algorithm for studying cooperative transitions in DNA

The origin of the A to B transition in DNA fibers and films

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